Biology

A set of preparatory actions on biological data was launched for a limited set of Sea Basins. The main objective of the biology project was the development of an online marine biological data portal allowing the access and download of marine biological data across Europe. The biological lot focused on gathering available information and on the temporal and spatial distribution of species composition, abundance and biomass of phytoplankton, zooplankton, angiosperms, macroalgae, invertebrate bottom fauna, bird communities, sea mammals and reptiles. The final report of that period is available online.

A consortium of 21 agencies, institutions and organisations that came together in the preparatory phase of EMODnet Biology delivered data, metadata and data products of surveys in the water column and on the sea bed from phytoplankton, zooplankton, angiosperms, macroalgae, benthos, birds, mammals, reptiles and fish occurring in European marine waters. This work was carried out also to support environmental legislations such as the MSFD (Marine Strategy Framework Directive).

A consortium of 22 agencies, institutions and organisations built further on the work carried out in the previous phase of EMODnet Biology. They carried on delivering data, metadata and data products of surveys in the water column and on the sea bed from phytoplankton, zooplankton, angiosperms, macroalgae, benthos, birds, mammals, reptiles and fishes occurring in European marine waters. And continued supporting environmental legislations (MSFD, etc.).

The consortium comprises 23 organisations, with four partners qualified as IODE Associated Data Units (ADU) and ten others as IODE National Oceanographic Data Centres (NODC). The partnership is geographically distributed and includes all European OBIS nodes (EurOBIS, MedOBIS , OBIS UK , OBIS Black Sea ). Collaboration with other international initiatives is also ensured via the consortium with the inclusion of e.g., IODE and ICES.

This phase will see an expansion of our web services, the implementation of management practices for other types of data like -omics and images and the migration to the Central Portal. Several new data products will be created and made freely available and a closer engagement with our stakeholders will ensure that our work will better answer their requirements.

The consortium is composed of 23 organisations with nine partners qualified as IODE National Oceanographic Data Centres (NODC) and four as IODE Associated Data Units (ADU). As in previous Phases, the partnership is geographically distributed across Europe and includes all European OBIS nodes (EurOBIS, (EurOBIS, MedOBIS , OBIS UK , OBIS Black Sea ). Collaboration with other international initiatives is also ensured via the consortium with the inclusion of e.g., IODE and ICES. Collaboration with other OBIS nodes, technical, data republication via EMODnet Biology is ensured via informal contacts. The collaboration currently focuses but is not limited to AntOBIS  (Antarctic node), Caribbean OBIS , OBIS Deep Sea , OBIS SeaMap , OBIS Kenya  and Oceans Past Initiative .

Following the centralisation work that was completed in January 2023, this new Phase will focus on maintaining and improving our webservices so users can access our data and products. We will also continue to develop our data infrastructure to accommodate for the publication of new types of data and will have a number of actions to better engage with our stakeholders as well as create products that can best address their needs.

Objectives

WP1 is set up to provide support to the whole project in terms of coordination and ensuring that all deliverables and objectives are met within the timelines proposed in the tender and also in this proposal. This WP will focus on Task 8: Monitor quality/performance and deal with user and is also responsible for organising project meetings with all parties involved, attending the EMODnet network meetings, as well as other events, e.g. conferences, workshops, seminars, etc., for which an invitation is received or participation required. Another main objective is ensuring that reporting is submitted according to the tender specifications, with guidance provided by the EMODnet Secretariat.

Methodology & activities

In order to achieve the objectives as included above, several Actions are planned for Phase V:

• Action 1.1 Usage of service monitoring via indicators (Lead: VLIZ);
• Action 1.2 Maintenance of centralised EMODnet catalogue of products (Lead: VLIZ, Partner: INRAE);
• Action 1.3 User feedback and support to the Centralised EMODnet helpdesk (Lead: VLIZ);
• Action 1.4 EMODnet Biology consortium meetings (Lead: VLIZ, Partners: INRAE, OGS);
• Action 1.5 EMODnet meetings/events (Lead: VLIZ, Partners: INRAE, OGS);
• Action 1.6 End of Phase Handover (Lead: VLIZ).

Deliverables

• D1.1.1 Quarterly Progress reports (M4-M24);
• D1.1.2 Interim report 10 May 2024 (M12);
• D1.1.3 Final Report 10 May 2025 (M24);
• D1.2.1 Update of EMODnet Biology data products via the EMODnet CP catalogue (M12, M24);
• D1.3.1 Monitoring user feedback via EMODnet JIRA (M0-M24);
• D1.3.2 Operation of the EMODnet CP helpdesk (M0-M24);
• D1.4.1 Minutes from the three project meetings (kick off, annual and final) (M1, M12, M24);
• D1.5.1 Participation in the EMODnet Steering Committee meetings (M0-M24);
• D1.5.2 Participation in the EMODnet Open Conference (M0-M24);
• D1.6.1 Appropriate mechanisms and guidelines for handover (M24).

Objectives

The main objective for WP2 is defined by Task 1- Maintain and improve a common method of access to data held in repositories, which will be addressed through the planning of various actions.

Methodology & activities

All efforts, data and outcomes of all previous phases of EMODnet Biology will feed into Phase V and the outputs planned will be split in five main Actions:

• Action 2.1 Data interoperability (Lead: VLIZ; Partners: OGS; Subcontractors: Aarhus, Deltares, HCMR, ICES, IEO, IH Cantabria, ILVO, IMR, IPMA, MARIS, MBA, NIOZ, Pangaea, SMHI, SYKE);
• Action 2.2 Streamline data holdings through Cloud technologies (Lead: VLIZ)
• Action 2.3 Evaluation of data restrictions (Lead: VLIZ; Partners: OGS; Subcontractors: Aarhus, Deltares, HCMR, ICES, IEO, IH Cantabria, ILVO, IMR, IPMA, MARIS, MBA, NIMRD, NIOZ, Pangea, SMHI, SYKE)
• Action 2.4 Data training workshops (Lead: HCMR; Partners: VLIZ)
• Action 2.5 Publication of omics data (Lead: VLIZ)

Output (Deliverables)

• D2.1.1 Maintenance of adequate mechanisms to ensure data are interoperable (M0-M24);
• D2.1.2 Report on the standardisation and integration of datasets published during the Phase (M24);
• D2.2.1 Summary on consortium data flows (M6);
• D2.3.1 Plan to optimise procedures to make restricted data available to users (M0-M24);
• D2.4.1 Workshop on use of Zooniverse for data digitisation through citizen science (M6);
• D2.4.2 Data training workshop for Mediterranean organisations (M6);
• D2.4.3 Report on the availability of data following the workshops (M22);
• D2.5.1 Guidance for data management practices applied to omics data (M0-M24).

Objectives

WP3 is set up to address Task 2: Construct products from one or more data sources that provide users with information about the distribution and quality of parameters in time and space. Building on previous Phases, WP3 will continue to create distribution maps targeting groups of species, as well as presence/absence maps, both of which can be queried, subset and downloaded via the EMODnet Central Portal viewer.

WP3 will develop efforts to maximize the uptake of existing and new data products by end users. This will be achieved by raising awareness of existing products, provide training materials in form of tutorials to manipulate and visualize EMODnet products using the existing R packages developed in Phase III and IV, and by co-creation of data product needs with stakeholders. The tender also requires the creation of products targeting species migration routes, in particular seabirds and cetaceans. Although there have been specific efforts made to increase the amount of data in EMODnet Biology for these two groups of species, the volume of data is still considered too limited to create sound and robust products for these taxa. Another constraint is that the current state-of-the-art for modelling distributions of these taxa uses individual movement data and highly sophisticated statistical analysis that is beyond the scope of this tender. Specific new actions will be taken to increase the data availability of these taxa by involving experts, by assessing the data sources of existing external products and indicators, and assessing the possibility of hosting these external products in EMODnet Biology.

During Phase V, a number of changes were implemented concerning data and product formatting, owing to the centralisation of the EMODnet services. Guidance for this was provided to all WP3 members on how to create their products in order to facilitate their incorporation in the EMODnet Central Portal Viewer. In Phase V we will continue with this approach and will adjust the guidance following the input of the EMODnet Secretariat, Central Portal team and any decisions resulting from the EMODnet Steering Committee.

Methodology & activities

In order to achieve the expected outputs, the work will be split in three main Actions:

• Action 3.1 Evaluation of data products from previous Phases (Lead: INRAE; Partner: OGS, VLIZ; Subcontractors: Cefas, Deltares, ICES, IH Cantabria, ILVO, MBA, NIMRD, NIOZ, SMHI, SYKE, UkrSCES, ULiège, U Sheffield);
• Action 3.2 Community calls (Lead: INRAE; Partner: VLIZ; Subcontractors: Cefas, Deltares, IH, Cantabria, NIOZ, SMHI, ULiège, U Sheffield);
• Action 3.3 Data product creation (Lead: INRAE; Partner: VLIZ; Subcontractors: Cefas, Deltares, IH Cantabria, NIOZ, SMHI, ULiège, U Sheffield).

Deliverables

• D3.1.1 Internal WP3 and WP4 Workshop 10 Sep 2023 (M4);
• D3.2.1 Quarterly community calls (M3-M24);
• D3.3.1 Liaison with external entities targeting seabird and cetacean migration outputs (M0-M24);
• D3.3.2 Data product creation (M0-M24).

Objectives

WP4 will cover three Tasks, more specifically: Task 5. Contributing static content to dedicated spaces in the Central Portal, Task 6: Ensure the involvement of Regional Sea Conventions RSC and Task 7: Contribute to the implementation of the EU legislation and broader initiatives for open data. Building on the expertise and connections developed in previous Phases, several actions will be put in place to ensure that the Tasks are achieved.

Methodology & activities

The Actions proposed are as follow:

• Action 4.1 Provide and update content to the EMODnet Central Portal (Lead: VLIZ; Partner: OGS; Subcontractors: ICES, ILVO, MBA, NIMRD, SYKE);
• Action 4.2 Interaction with the RSCs and ICES (Lead: OGS; Subcontractors: ICES, ILVO, NIMRD, SYKE);
• Action 4.3 Liaison with relevant EU initiatives, projects and parties (Lead: OGS; Partner: VLIZ; Subcontractors: ICES, ILVO, MBA, NIMRD, SYKE);
• Action 4.4 Ensure compatibility with INSPIRE Directive (Lead: OGS, Partner: VLIZ).

In previous Phases various lines of work were established to ensure that EMODnet Biology assets, e.g. metadata, data and data products are compliant with the INSPIRE directive. In Phase V the proposed work will be towards a better engagement with EU Member States, more specifically in providing support with their reporting obligations regarding, for example MSFD indicators.

Deliverables

• D4.1.1 Update connectivity maps and identification of stakeholder community (M4) ;
• D4.1.2 Informative material based 4.2.2 published in the EMODnet CP (M12);
• D4.1.3 Informative material based on the 4.2.3 outcomes (M14);
• D4.1.4 Informative material based on the 4.3.1 outcomes (M24);
• D4.1.5 Publication of four Use Cases (M6, M12, M18, M24);
• D4.1.6 Publication of written documents (M0-M24);
• D4.2.1 Engagement plan for each RSC (M6);
• D4.2.2 Questionnaire to inform about what data & products EMODnet Biology offers and to collect stakeholder needs (M6);
• D4.2.3 Workshop with RSCs to understand major needs (M12);
• D4.2.4 Report on progress for the publication of fisheries survey data (M24);
• D4.3.1 Workshop with representatives of major recent and current European Research Projects and initiatives to share experience and knowledge in biodiversity monitoring and assessment and in data, tools and services (M18);
• D4.3.2 Participation in TG DATA meetings (M0-M24);
• D4.4.1 Ensure compatibility with INSPIRE Directive (data, metadata, data products) (M0-M24);
• D4.4.2 Report on the activities to support EU Member States regarding their reporting obligations (M24).

Objectives

WP5 is responsible for fulfilling Task 3: Develop procedures for machine-to-machine connections to data and data Products and Task 4: Contribute data, data products and content to EMODnet Central Portal that allows users to find, view and download data and data products, as required in the tender document. VLIZ is the WP lead and will be supported with the technical capacity of other organisations (some already identified and others will be identified once the contract is signed) for accomplishing the objectives therein. The work expected for Task 3 should result in the maintenance and further development of Application Programme Interfaces (APIs), such as web services, to allow for metadata, data and data products to be found, viewed and downloaded by applications running on other machines. An alignment of the plan and solutions with the other thematic lots should be achieved to abolish barriers for users and operating systems. The plan defined for Task 3 shall be discussed during the EMODnet Steering Committee meetings and validated by the Contracting authority before it can be implemented. Within Task 4, the main objectives focuses on ensuring that metadata are easily discoverable for cataloguing and INSPIRE services, that data and data products can be discovered, viewed, downloaded and accessed by EMODnet Central Portal in a straightforward manner and with minimum steps and to ensure that coherence with the other thematic groups is achieved by participation in regular meetings of a Technical Working Group.

Description of work

Four Actions are planned for this WP and their detailed description is as follows:

• Action 5.1: Extend interoperability and data types (Lead: VLIZ, Subcontractor: MARIS);
• Action 5.2: Implement machine-to-machine connections to data and data products (Lead: VLIZ);
• Action 5.3: EMODnet Biology Technical Infrastructure maintenance and operational management (Lead: VLIZ);
• Action 5.4: Contribute data, data products and content to EMODnet Central Portal that allows users to find, view and download data and data products (Lead: VLIZ).

Deliverables

• D5.1.1 Streamlining semantic interoperability (M0-M20);
• D5.1.2 Integration of omics data into the data model (M16);
• D5.1.3 Roadmap for marine biodiversity data (M24);
• D5.2.1 M2M communication plan and solutions (M0-M24);
• D5.3.1 Operational web services (M0-M24);
• D5.3.2 Technology stack upgrades (M24);
• D5.3.3 Technical maintenance of procedures for ingestion of data from the data providers (M0-M24);
• D5.3.4 Development and implementation of procedures to publish omics data (M24);
• D5.4.1 Synchronisation of all data and data products metadata to the EMODnet CP catalogue (GeoNetwork) (M0-M24);
• D5.4.2 All data and products available through the EMODnet CP (M2-M24);
• D5.4.3 Participation in the EMODnet TWG meetings (M0-M24);
• D5.4.4 Maintenance and development of API used to query EMODnet Biology layers available via the EMODnet CP viewer (M0-M24).

• Occurrence data (species observations) as Web Feature Service (WFS); Additional measurements, linked to the occurrence data as Web Feature Service (WFS);
• Retrieve data of the gridded abundance data products as WFS/WMS;
• Using the AphiaID to query by (biological) taxonomy;
• Using the IMISDasID to query by metadata dataset;
• Examples of EMODnet Biology Data applications written in R.

The Integrated Publishing Toolkit (IPT) , a freely available open source web application using the Darwin Core standard, will make it easy to share biodiversity-related data and information with the EMODnet portal.

The Quality Check (QC) tool was created to support data providers in assessing the quality of their datasets prior to submission. It can be used either through an Rshiny application or as an R package. Please check our video tutorial on how to use this tool and understand its output.

Training originally set up for EMODnet Biology Partners, opened up for self-enrolment since the November 2023. It allows access to scientists & data managers to use the available material to learn how to format, standardise and quality control their biodiversity data for submission to EMODnet Biology.
You can enrol and follow the course on OTGA (Ocean Teacher Global Academy): classroom.oceanteacher.org/enrol/index.php?id=958

The R package , partially funded by EMODnet Biology, is designed to make all EMODnet thematic lots’ raster data layers easily accessible in R. The package allows users to query information on and download data from all available EMODnet Web Coverage Service (WCS) endpoints directly into their R working environment.

The R package , created by EMODnet Biology partners, is designed to make all EMODnet thematic lots’ vector data layers easily accessible in R. The package allows users to query information on and download data from all available EMODnet Web Feature Service (WFS) endpoints directly into their R working environment.

BTrait was developed in the scope of EMODnet Biology to facilitates working with species density data, combined with species traits in R. It allows users to query the linked datasets (species density and trait data) and visualise it with an interactive shiny application.

The following file includes information about the mandatory and recommended fields for data submission to EMODnet Biology. Please contact us via bio@emodnet.eu if you have any questions.

EMODnet Biology: List of terms delivered for each download option